Despite broader taxon sampling and multilocus character sets, analyses of extant seed plant relationships have not provided a clear resolution of the relative positions of the extant seed plant lineages: angiosperms, gnetophytes, conifers, cycads, and ginkgo. The nature of the cycad-ginkgo relationship and, in particular, the placement of gnetophytes as either sister to angiosperms (the anthophyte hypothesis), sister to all other extant seed plants (the gne-sister hypothesis), sister to the conifers (the gnetifer hypothesis), or sister to the Pinaceae (the gne-pine hypothesis), have been controversial. Analyses have proved sensitive to methodological biases that are assumed to result, at least in part, from rate heterogeneity in the sampled loci. One potential solution to this problem is to increase the number of loci. In this study, we bring the fruits of plastid genomics to bear upon this question, utilizing an 83-gene data set to explore questions of bias and the effects of outgroup sampling. Taxon sampling includes three pteridophytes, nine angiosperms, and 13 gymnosperms (ginkgo, three cycads, three gnetophytes, and six conifers) drawn from published and experimental sources. Preliminary rooted analyses using all ungapped positions show that methods most likely to be confounded by long branch attraction (e.g., maximum parsimony) support a ginkgo+cycad sister group and the gne-sister hypothesis, whereas analyses less likely to suffer artifacts due to rate heterogeneity (maximum likelihood, Bayesian inference) support cycads as the first gymnosperm branch followed by ginkgo and place the gnetophytes within conifers as sister to the Conifer II group (non-Pinaceae conifers) with strong bootstrap and posterior probability support. SH tests indicate that the anthophyte, gne-sister, and gnetifer hypotheses are all significantly less likely (p < 0.001), but neither the ginkgo-cycad sister group nor the gne-pine hypothesis can be rejected with these data.